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ABLIM3 actin binding LIM protein family member 3 [ Homo sapiens (human) ]

Gene ID: 22885, updated on 8-Dec-2018

Summary

Official Symbol
ABLIM3provided by HGNC
Official Full Name
actin binding LIM protein family member 3provided by HGNC
Primary source
HGNC:HGNC:29132
See related
Ensembl:ENSG00000173210 MIM:611305
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HMFN1661
Summary
This gene encodes a member of the actin-binding LIM (abLIM) family of proteins. These proteins are characterized by an N-terminal LIM domain and a C-terminal dematin-like domain. The encoded protein interacts with actin filaments and may be a component of adherens junctions in several cell types. A variant of this gene may be associated with pain sensitivity in male human patients. [provided by RefSeq, Sep 2016]
Expression
Broad expression in fat (RPKM 33.5), heart (RPKM 19.5) and 14 other tissues See more
Orthologs

Genomic context

See ABLIM3 in Genome Data Viewer
Location:
5q32
Exon count:
25
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (149141447..149260439)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (148521054..148640002)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene SH3TC2 divergent transcript Neighboring gene RNA, 7SK small nuclear pseudogene 145 Neighboring gene actin filament associated protein 1 like 1 Neighboring gene GRPEL2 antisense RNA 1 Neighboring gene GrpE like 2, mitochondrial

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Pathways from BioSystems

  • Axon guidance, organism-specific biosystem (from KEGG)
    Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, conserved biosystem (from KEGG)
    Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • DCC mediated attractive signaling, organism-specific biosystem (from REACTOME)
    DCC mediated attractive signaling, organism-specific biosystemThe DCC family includes DCC and neogenin in vertebrates. DCC is required for netrin-induced axon attraction. DCC is a transmembrane protein lacking any identifiable catalytic activity. Protein tyrosi...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • Netrin-1 signaling, organism-specific biosystem (from REACTOME)
    Netrin-1 signaling, organism-specific biosystemNetrins are secreted proteins that play a crucial role in neuronal migration and in axon guidance during the development of the nervous system. To date, several Netrins have been described in mouse a...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin filament binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
actin cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
 
cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
lamellipodium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lamellipodium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein targeting to mitochondrion HMP PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
actin cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stress fiber IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
actin-binding LIM protein 3
Names
abLIM-3

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_051566.1 RefSeqGene

    Range
    5001..123993
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301015.2NP_001287944.1  actin-binding LIM protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001287944.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC091940, AK225769, AK289736, BP285049
    Consensus CDS
    CCDS4294.1
    UniProtKB/Swiss-Prot
    O94929
    Related
    ENSP00000425394.1, ENST00000506113.5
    Conserved Domains (6) summary
    smart00153
    Location:648683
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274647
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  2. NM_001301018.2NP_001287947.1  actin-binding LIM protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001287947.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AB020650, AC091940, AK225769, DA669720, DQ413174
    Consensus CDS
    CCDS78069.1
    UniProtKB/Swiss-Prot
    O94929
    UniProtKB/TrEMBL
    A0A0C4DGA7
    Conserved Domains (6) summary
    smart00153
    Location:615650
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274614
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  3. NM_001301027.2NP_001287956.1  actin-binding LIM protein 3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an additional exon in the 5' region, which results in translation initiation at a downstream start codon, and lacks several in-frame exons in the 3' coding region, compared to variant 1. The resulting isoform (3) has a distinct N-terminus and lacks two internal segments, compared to isoform 1.
    Source sequence(s)
    AC091940, AK225769, AL833021, BC014463, BP285049
    UniProtKB/Swiss-Prot
    O94929
    Conserved Domains (5) summary
    smart00153
    Location:545580
    VHP; Villin headpiece domain
    cd09329
    Location:159210
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:218273
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:282544
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
    cl02475
    Location:121142
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  4. NM_001301028.2NP_001287957.1  actin-binding LIM protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001287957.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks several in-frame exons and has an alternate splice site in the 3' coding region, compared to variant 1. The resulting isoform (4) lacks two internal segments and has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC091940, AK225769, BC001665, BP285049
    Consensus CDS
    CCDS78071.1
    UniProtKB/Swiss-Prot
    O94929
    Related
    ENSP00000421183.1, ENST00000504238.5
    Conserved Domains (5) summary
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274535
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  5. NM_001345858.1NP_001332787.1  actin-binding LIM protein 3 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC012613, AC091940, AL833021
    UniProtKB/Swiss-Prot
    O94929
    Conserved Domains (6) summary
    smart00153
    Location:599634
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274598
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  6. NM_001345859.1NP_001332788.1  actin-binding LIM protein 3 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC012613, AC091940, AL833021
    Consensus CDS
    CCDS87335.1
    UniProtKB/Swiss-Prot
    O94929
    Related
    ENSP00000315841.7, ENST00000326685.11
    Conserved Domains (6) summary
    smart00153
    Location:553588
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274552
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  7. NM_001345860.1NP_001332789.1  actin-binding LIM protein 3 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC012613, AC091940, AL833021
    UniProtKB/Swiss-Prot
    O94929
    Conserved Domains (6) summary
    smart00153
    Location:537572
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274536
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  8. NM_001345861.1NP_001332790.1  actin-binding LIM protein 3 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC012613, AC091940, AL833021
    Consensus CDS
    CCDS87335.1
    UniProtKB/Swiss-Prot
    O94929
    Conserved Domains (6) summary
    smart00153
    Location:553588
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274552
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  9. NM_014945.4NP_055760.1  actin-binding LIM protein 3 isoform 1

    See identical proteins and their annotated locations for NP_055760.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal segment in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform 1.
    Source sequence(s)
    AC091940, AK225769, AK289736, BC001665, BP285049
    Consensus CDS
    CCDS4294.1
    UniProtKB/Swiss-Prot
    O94929
    Related
    ENSP00000310309.7, ENST00000309868.11
    Conserved Domains (6) summary
    smart00153
    Location:648683
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274647
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    149141447..149260439
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005268394.2XP_005268451.1  actin-binding LIM protein 3 isoform X3

    See identical proteins and their annotated locations for XP_005268451.1

    Conserved Domains (6) summary
    smart00153
    Location:586621
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274585
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  2. XM_011537609.3XP_011535911.1  actin-binding LIM protein 3 isoform X6

    Conserved Domains (5) summary
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274435
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  3. XM_024446006.1XP_024301774.1  actin-binding LIM protein 3 isoform X5

    Conserved Domains (5) summary
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274351
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  4. XM_024446003.1XP_024301771.1  actin-binding LIM protein 3 isoform X1

    Related
    ENSP00000420855.1, ENST00000508983.5
    Conserved Domains (6) summary
    smart00153
    Location:615650
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274614
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  5. XM_024446004.1XP_024301772.1  actin-binding LIM protein 3 isoform X2

    Conserved Domains (6) summary
    smart00153
    Location:599634
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274598
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
  6. XM_024446005.1XP_024301773.1  actin-binding LIM protein 3 isoform X4

    Conserved Domains (6) summary
    smart00153
    Location:537572
    VHP; Villin headpiece domain
    cd09327
    Location:2374
    LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
    cd09328
    Location:79134
    LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
    cd09329
    Location:151202
    LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
    cd09330
    Location:210265
    LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
    pfam16182
    Location:274536
    AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM
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